- PDB-5ome: The cryofrozen atomic resolution X-ray crystal structure of the r... -
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Open data
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Basic information
Entry
Database: PDB / ID: 5ome
Title
The cryofrozen atomic resolution X-ray crystal structure of the reduced form (Fe2+) perdeuterated Pyrococcus furiosus Rubredoxin in D2O (100K, 0.75 Angstrom resolution)
Components
Rubredoxin
Keywords
ELECTRON TRANSPORT / Perdeuterated rubredoxin / pyrococcus furiosus / atomic resolution / cryofrozen / reduced / iron
Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.12 Å3/Da / Density % sol: 41.98 % Description: bipyramid bright red (Fe3+), Subsequently reduced with Na2S2O3 to get transparent (Fe2+) crystal. X-ray data collection performed with helicoidal strategy over 180 degrees rotation.
Method to determine structure: AB INITIO PHASING / Resolution: 0.747→18.363 Å / SU ML: 0.02 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 10.12 Details: Deuterium atoms are isotropic, protein atoms, Fe atom and solvent O atoms are anisotropic
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1214
2892
5.03 %
random
Rwork
0.111
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obs
0.1115
57545
85.72 %
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Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement step
Cycle: LAST / Resolution: 0.747→18.363 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
421
0
12
209
642
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.008
498
X-RAY DIFFRACTION
f_angle_d
1.01
687
X-RAY DIFFRACTION
f_dihedral_angle_d
17.92
191
X-RAY DIFFRACTION
f_chiral_restr
0.084
64
X-RAY DIFFRACTION
f_plane_restr
0.009
96
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
0.747-0.7593
0.2897
15
0.1935
261
X-RAY DIFFRACTION
9
0.7593-0.7723
0.14
50
0.1481
865
X-RAY DIFFRACTION
29
0.7723-0.7864
0.143
59
0.1361
1360
X-RAY DIFFRACTION
45
0.7864-0.8015
0.1257
83
0.125
1848
X-RAY DIFFRACTION
61
0.8015-0.8179
0.1252
142
0.1124
2226
X-RAY DIFFRACTION
75
0.8179-0.8357
0.1046
130
0.111
2640
X-RAY DIFFRACTION
87
0.8357-0.8551
0.1109
166
0.1058
2831
X-RAY DIFFRACTION
95
0.8551-0.8765
0.1075
135
0.1008
3003
X-RAY DIFFRACTION
100
0.8765-0.9002
0.1136
153
0.0936
3025
X-RAY DIFFRACTION
100
0.9002-0.9267
0.102
162
0.0914
2991
X-RAY DIFFRACTION
100
0.9267-0.9566
0.102
153
0.0899
3027
X-RAY DIFFRACTION
100
0.9566-0.9908
0.1112
171
0.0856
3013
X-RAY DIFFRACTION
100
0.9908-1.0304
0.0969
151
0.087
3034
X-RAY DIFFRACTION
100
1.0304-1.0773
0.0942
176
0.0853
2994
X-RAY DIFFRACTION
100
1.0773-1.1341
0.0926
149
0.0875
3048
X-RAY DIFFRACTION
100
1.1341-1.2052
0.1019
176
0.0936
3017
X-RAY DIFFRACTION
100
1.2052-1.2982
0.1048
184
0.1041
3022
X-RAY DIFFRACTION
100
1.2982-1.4288
0.1148
161
0.1164
3053
X-RAY DIFFRACTION
100
1.4288-1.6354
0.1324
146
0.1208
3097
X-RAY DIFFRACTION
100
1.6354-2.06
0.1291
168
0.13
3096
X-RAY DIFFRACTION
99
2.06-18.3683
0.1543
162
0.126
3202
X-RAY DIFFRACTION
98
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